As a 4X game, I generally like the ship-to-ship combat how it is. If I want more tactical battles, I'll play Starfleet Command, or pull out dice and SSDs and play Starfleet Battles...
I think it might be intriguing to make a few changes to GalCiv2 ship-to-ship combat though:
1. Morale impacts on battles... Low morale could see ships attempting to flee, mutinees, defections...
2. Option to ATTEMPT to disengage from battle if not in orbit. This would only apply if you had available movement points prior to entering the battle.
3. I think the option to carry a ship-board-marines module so you could board and take-over enemy ships would be interesting. Have a requirement you to get that ship back to a home planet to repair it. This would all require an additional branch of tech to research for the offensive and defensive aspects of this.
4. Similar to #3, the idea of 'postures'. Could a defensive/peaceful ("Good"?) stance be set on ships so they focus on the destruction/disabling of enemy weapon systems. and/or engines? Make it so enemy ships don't/can't repair within 'x' parsecs of worlds they're at war with.
Anyway, nothing to say my ideas are any more valid than anyone else's but here's my 2 cents (1.7 cents US).